Both surface water temperatures and the intensity of thermal stratification have increased recently in large lakes throughout the world. Such physical changes can be accompanied by shifts in plankton community structure, including changes in relative abundances and depth distributions. Here we analyzed 45 years of data from Lake Baikal, the world's oldest, deepest, and most voluminous lake, to assess long-term trends in the depth distribution of pelagic phytoplankton and zooplankton. Surface water temperatures in Lake Baikal increased steadily between 1955 and 2000, resulting in a stronger thermal gradient within the top 50 m of the water column. In conjunction with these physical changes our analyses reveal significant shifts in the daytime depth distribution of important phytoplankton and zooplankton groups. The relatively heavy diatoms, which often rely on mixing to remain suspended in the photic zone, shifted downward in the water column by 1.90 m y-1, while the depths of other phytoplankton groups did not change significantly. Over the same time span the density-weighted average depth of most major zooplankton groups, including cladocerans, rotifers, and immature copepods, exhibited rapid shifts toward shallower positions (0.57–0.75 m y−1). As a result of these depth changes the vertical overlap between herbivorous copepods (Epischura baikalensis) and their algal food appears to have increased through time while that for cladocerans decreased. We hypothesize that warming surface waters and reduced mixing caused these ecological changes. Future studies should examine how changes in the vertical distribution of plankton might impact energy flow in this lake and others.